7  Find Markers

Finds markers (differentially expressed genes) for each of the UMAP blobs

Seurat object created by Chloe using the code from the previous documents

An object of class Seurat 
50776 features across 52784 samples within 3 assays 
Active assay: SCT (23656 features, 0 variable features)
 3 layers present: counts, data, scale.data
 2 other assays present: RNA, integrated
 2 dimensional reductions calculated: pca, umap

7.1 All cells

7.1.1 UMAP

Comparison of UMAPs previously annotated using ScType and clustered with Seurat.

7.1.2 Top marker genes per cluster

Normalized expression values from the SCT assay in your Seurat object for the marker genes

The SCT assay stores log-normalized residual expression values from SCTransform. Values are continuous and typically centered around 0

7.2 Cleaned dataset

After profound contemplation, the committee of experts decided to eliminate clusters 18, 21, 30, and 31 based on the markers represented in the violin plot.

7.2.1 UMAP

7.2.2 Marker genes (chatGPT 5)

For each Seurat cluster, the top differentially expressed genes were selected based on two criteria:
1. The gene had to be expressed in more than 30% of the cells in the cluster (pct.1 > 0.3), ensuring that selected genes represent markers broadly expressed within the cluster rather than being driven by rare subpopulations.

2. Among those genes, we ranked by the average log₂ fold change (avg_log2FC) relative to all other clusters and selected the top 20 genes with the highest positive fold change. This favors genes with the most specific and robust upregulation in the cluster of interest.

7.2.2.1 Cluster 0

Gene	Cell	Subtype	Notes
Nfkbiz	microglia	activated/pro-inflammatory	NF-κB regulator induced by TLR signaling; enriched in LPS/DAM microglia.
Bcl2a1b	microglia	activated/pro-survival	Anti-apoptotic BCL2 family; high in myeloid cells under inflammation.
Tnf	microglia	activated/pro-inflammatory	Canonical cytokine from activated microglia; drives NF-κB responses.
Bcl2a1d	microglia	activated/pro-survival	Myeloid-biased anti-apoptotic factor; up in inflammatory states.
Mapkapk2	microglia	stress/p38-MK2 pathway	p38 target regulating TNF/IL-1β mRNA stability in myeloid cells.
Ier3	microglia	immediate-early activated	Early stress/immune response gene induced by NF-κB.
Cd14	microglia	activated/DAM	Myeloid LPS co-receptor; elevated in DAM/activated microglia.
Ccrl2	microglia	activated/chemokine-responsive	Atypical chemokine receptor in myeloid lineages; rises with activation.
Il1b	microglia	activated/pro-inflammatory	Hallmark cytokine of inflammatory microglia.
Rel	microglia	activated/NF-κB	c-Rel NF-κB subunit; immune-cell biased activation marker.
Mir155hg	microglia	activated/DAM	Host gene for miR-155; strong in activated microglia/macrophages.
Dennd4a	microglia	activated/vesicle trafficking	Rab10 GEF; broad gene but induced in myeloid activation and trafficking.
Cd86	microglia	antigen-presenting	Costimulatory molecule up in MHC-II⁺ microglia.
Rab7b	microglia	activated/endolysosomal	Macrophage-enriched small GTPase modulating TLR trafficking.
Myo1e	microglia	activated/cytoskeletal	Myosin 1e enriched in myeloid cells; supports phagocytosis.
Osbpl8	microglia	lipid-handling/DAM	Oxysterol-binding protein involved in cholesterol/LDL trafficking.
Whrn	neuron	unspecified neuron	Scaffolding protein (whirlin); neuronal/sensory enrichment relative to glia.
Pdgfb	endothelial	capillary/vascular	Endothelial-derived PDGFB recruits PDGFRβ⁺ pericytes; vascular marker.
Bcl2l11	microglia	stress/apoptosis-prone	Pro-apoptotic BIM; induced by cytokine stress in myeloid cells.
Cd180	lymphocyte	B cell	RP105; B-cell marker rarely seen in brain, suggests infiltrating B cells.

Most genes point to activated microglia with a pro-inflammatory/DAM profile (NF-κB, TLR, cytokine, lipid-handling, and endolysosomal programs). One clear vascular marker (Pdgfb) indicates endothelial signal. Cd180 suggests a minor B-cell presence. Whrn and Dennd4a are less specific but fit best with neuronal and activated-myeloid contexts, respectively.

7.2.2.2 Cluster 1

Gene	Cell	Subtype	Notes
Ctsz	microglia	homeostatic/lysosomal	Cathepsin Z; lysosomal protease enriched in microglia/macrophages.
Serpine2	neuron	excitatory neuron (layer-enriched)	Serine protease inhibitor; enriched in cortical neurons, involved in synaptic remodeling.
Hif1a	microglia	hypoxia-responsive	Hypoxia-inducible TF; upregulated in myeloid cells under low O₂.
Or5v1b	neuron	olfactory receptor neuron	Olfactory receptor gene; sensory neuron-specific.
Fcgr3	microglia	activated/DAM	Fc gamma receptor III; immune complex receptor in microglia/macrophages.
Hexb	microglia	homeostatic	Lysosomal β-hexosaminidase; strong canonical microglia marker.
Baiap2l2	neuron	excitatory neuron (spine-associated)	Actin-binding protein enriched in synaptic structures.
Sirpa	microglia	homeostatic/inhibitory signaling	“Don’t eat me” receptor; high in microglia for synaptic pruning control.
Egln3	microglia	hypoxia-responsive	Prolyl hydroxylase induced by hypoxia in glia/myeloid cells.
Adarb1	neuron	excitatory neuron (RNA editing)	RNA-editing enzyme; neuronal, especially in cortex/hippocampus.
P4ha1	microglia	hypoxia/fibrosis-associated	Collagen prolyl 4-hydroxylase; hypoxia-inducible in activated microglia.
Gpr183	microglia	chemotactic/activated	Oxysterol receptor EBI2; microglia/macrophage migration regulator.
Gcnt2	microglia	glycosylation-associated	Glycosyltransferase; found in myeloid cells including microglia.
Gm56614	unclassified	uncharacterized	Predicted gene; expression context-dependent.
H1f3	oligodendrocyte	immature/OPC	Histone H1 variant enriched during oligodendrocyte differentiation.
Marchf3	microglia	antigen-presentation-associated	E3 ubiquitin ligase regulating immune receptor turnover.
Immp2l	neuron	mitochondrial processing	Inner mitochondrial membrane peptidase; neuronal enrichment.
Tcap	muscle cell	skeletal muscle	Titin-cap; usually non-CNS, could be perivascular muscle contamination.
Gm57375	unclassified	uncharacterized	Predicted gene; cell-type assignment unclear.
Tex14	germ cell	testis-specific	Germ cell protein; likely ambient RNA or contamination.

Cluster 1 contains a strong microglial signature, with many homeostatic and activated/DAM markers (Ctsz, Hexb, Sirpa, Fcgr3, Gpr183, Marchf3) and a hypoxia-responsive profile (Hif1a, Egln3, P4ha1). Several neuronal genes (Serpine2, Baiap2l2, Adarb1, Immp2l) suggest either mixed-cell contamination or close neuronal interaction. A few genes (Tcap, Tex14, Gm56614, Gm57375) are likely ambient RNA or non-CNS contaminants. Overall, this cluster most likely represents hypoxia-responsive activated microglia with some mixed neuronal signal.

7.2.2.3 Cluster 2

Gene	Cell	Subtype	Notes
Tmem119	microglia	homeostatic microglia	Canonical microglial marker defining resident lineage.
Tnfaip3	microglia	activated/NF-κB feedback	A20; NF-κB negative regulator induced by TLR/cytokines.
Ppp1r15a	microglia	stress/ISR	GADD34; integrated stress response, seen in activated myeloid cells.
Entpd1	endothelial	capillary/endothelial	CD39; high in brain endothelium and perivascular niche.
Dapp1	microglia	TLR/BCR adaptor	Myeloid adaptor enhancing PI3K signaling; induced with activation.
Pde3b	microglia	metabolic/anti-inflammatory	cAMP PDE enriched in myeloid cells, modulates cytokine output.
Pag1	microglia	lipid-raft/immune modulation	PAG/Cbp; Src-family signaling brake in immune cells including microglia.
Rasgef1b	microglia	LPS-inducible	RASGEF1B up in macrophage/microglia after TLR stimulation.
Agmo	microglia	lipid catabolism	Alkylglycerol monooxygenase; myeloid lipid-handling/DAM programs.
Casp4	microglia	inflammasome-related	Inflammatory caspase family; noncanonical inflammasome pathway.
Mertk	microglia	phagocytic/DAM	TAM receptor for efferocytosis and myelin/amyloid clearance.
Dusp6	microglia	MAPK feedback	ERK phosphatase; activation-linked negative feedback in myeloid cells.
Adrb2	astrocyte	protoplasmic astrocyte	β2-adrenergic receptor enriched in astrocytes responding to NE.
Tgm2	microglia	DAM/phagocytic	Transglutaminase 2; elevated in disease-associated microglia.
Fchsd2	microglia	endocytic trafficking	Endocytosis/actin regulator; reported in activated myeloid cells.
Tbxas1	microglia	eicosanoid synthesis	Thromboxane synthase; arachidonic pathway in macrophage/microglia.
Slc8a1	neuron	excitatory neuron	NCX1; strong neuronal membrane exchanger, broad neuronal enrichment.
Gpr84	microglia	activated myeloid	Medium-chain fatty acid GPCR; robust in activated microglia.
Chst8	neuron	secretory/glycosylation	GalNAc sulfotransferase; neuronal secretory pathway enrichment.
Myc	microglia	cycling/activated	Proliferation/activation TF; seen in dividing/reactive microglia.

Most genes indicate activated microglia with DAM, phagocytic, lipid-handling, and NF-κB/stress feedback programs. A vascular signal appears via Entpd1. Adrb2 points to astrocytes. Slc8a1 and Chst8 support a minor neuronal component. Overall, cluster 2 aligns best with activated/phagocytic microglia with limited endothelial, astrocytic, and neuronal admixture.

7.2.2.4 Cluster 3

Gene	Cell	Subtype	Notes
Spp1	microglia	DAM/osteopontin⁺	Osteopontin; hallmark of Spp1⁺ disease-associated microglia.
H2-Aa	microglia	MHC-II⁺ antigen-presenting	Class II MHC; up in CD74⁺ APC-like microglia.
Itgax	microglia	CD11c⁺ DAM	CD11c; marks activated/DAM microglia.
Cst7	microglia	DAM/lysosomal	Cystatin F; elevated in phagocytic DAM.
H2-Eb1	microglia	MHC-II⁺ antigen-presenting	Class II MHC component; APC-like microglia.
Atp6v0d2	microglia	DAM/lysosomal acidification	V-ATPase subunit; osteoclast-like, up in DAM.
H2-Ab1	microglia	MHC-II⁺ antigen-presenting	Class II MHC; supports antigen presentation.
Cd74	microglia	MHC-II⁺ antigen-presenting	Invariant chain; high in APC-like microglia.
Dkk2	microglia	DAM/Wnt-modulatory	Wnt inhibitor; enriched in subsets of DAM.
Gpnmb	microglia	DAM/phagocytic	Glycoprotein NMB; robust in Trem2⁺ DAM.
Ccl6	microglia	activated myeloid	Chemokine enriched in inflammatory myeloid cells.
Ctsl	microglia	lysosomal	Cathepsin L; up in phagocytic/lysosomal programs.
Trem2	microglia	DAM/phagocytic	Central DAM receptor driving lipid sensing and clearance.
Cd63	microglia	endolysosomal/exosomal	Tetraspanin of late endosomes; increased with activation.
Fcrls	microglia	homeostatic-to-DAM transition	Microglia-enriched receptor retained across states.
B2m	microglia	MHC-I⁺ activated	β2-microglobulin; antigen presentation, activation marker.
Ctnna3	neuron	excitatory neuron	Adherens junction protein; neuronal adhesion molecule.
Tlr2	microglia	TLR-activated	Pattern-recognition receptor; up in activated microglia.
Malt1	microglia	NF-κB signaling	Paracaspase in CBM complex; immune activation.
Postn	perivascular fibroblast	reactive fibroblast	Periostin; ECM protein from meningeal/perivascular fibroblasts.

This set is dominated by a classic DAM/MHC-II⁺ microglial program (Spp1, Itgax, Trem2, Gpnmb, Cst7, Atp6v0d2, H2 genes, Cd74, Cd63, Tlr2, Malt1, Ccl6, B2m), indicating antigen-presenting, phagocytic, and lysosomal activation. Fcrls supports microglial identity across states. Ctnna3 suggests minor neuronal contamination. Postn points to a small perivascular fibroblast signal.

7.2.2.5 Cluster 4

Gene	Cell	Subtype	Notes
Qdpr	oligodendrocyte	mature myelinating	Enzyme in BH4 metabolism; enriched in oligodendrocytes.
A230001M10Rik	oligodendrocyte	mature myelinating	Predicted gene with strong oligodendrocyte expression in scRNA-seq atlases.
Aspa	oligodendrocyte	mature myelinating	Aspartoacylase; canonical oligodendrocyte marker.
Plekhh1	oligodendrocyte	mature myelinating	PlekHH1 expressed in oligodendrocytes, function in cytoskeleton regulation.
C030029H02Rik	oligodendrocyte	mature myelinating	Predicted transcript enriched in oligodendrocyte populations.
Tmem151a	neuron	excitatory neuron (layer 2/3)	Membrane protein highly expressed in certain cortical neurons.
Abca2	oligodendrocyte	mature myelinating	Lipid transporter highly enriched in myelin-forming oligodendrocytes.
Gm42756	unclassified	uncharacterized	Predicted gene; uncertain, possibly oligodendrocyte-enriched.
Tmem229a	neuron	excitatory neuron	TMEM229A found in neuronal clusters in mouse brain data.
Mast4	neuron	excitatory neuron	Microtubule-associated serine/threonine kinase; neuronal expression.
Efhd1	neuron	excitatory neuron	Calcium-binding mitochondrial protein enriched in neurons.
Dnajb2	neuron	excitatory neuron	Hsp40 co-chaperone; high neuronal expression.
Vldlr	neuron	excitatory neuron (Reelin pathway)	Very-low-density lipoprotein receptor in Reelin signaling; neuronal dendrite development.
Lrrn1	neuron	excitatory neuron	Leucine-rich repeat neuronal protein; cortical and hippocampal neurons.
Fign	neuron	excitatory neuron	Fidgetin; microtubule-severing enzyme enriched in neurons.
Ppp2r3a	neuron	excitatory neuron	PP2A regulatory subunit; broad neuronal enrichment.
4930420G21Rik	unclassified	uncharacterized	Predicted gene; unknown, likely neuronal expression pattern.
Jph4	neuron	excitatory neuron	Junctophilin-4; presynaptic calcium channel scaffolding protein.
Acyp2	neuron	excitatory neuron	Acylphosphatase; neuronal expression in brain.
5033421B08Rik	unclassified	uncharacterized	Predicted gene; unclear, possible neuronal bias.

Cluster 4 shows a mixed profile with a strong mature oligodendrocyte signature (Qdpr, Aspa, Abca2, Plekhh1, C030029H02Rik, A230001M10Rik) alongside a substantial set of neuronal markers (Tmem151a, Vldlr, Lrrn1, Jph4, Mast4, Efhd1). This pattern may reflect partial doublets or oligodendrocyte–neuron interactions in myelinated tracts. Uncharacterized predicted genes likely follow the main cell-type patterns observed.

7.2.2.6 Cluster 5

Gene	Cell	Subtype	Notes
Gm10790	unclassified	uncharacterized	Predicted transcript; limited annotation in brain datasets.
Ccr5	microglia	activated myeloid	Chemokine receptor on CNS myeloid cells; rises with inflammation.
P2ry12	microglia	homeostatic microglia	Canonical microglial GPCR; downregulated with activation.
Lpcat2	microglia	activated/inflammatory	Lipid-remodeling enzyme induced by LPS/TLR signaling in myeloid cells.
Siglech	microglia	homeostatic microglia	Mouse microglia marker in parenchyma; used for microglia-specific targeting.
A830008E24Rik	unclassified	uncharacterized	Predicted gene; cell-type bias unclear in brain.
Gm2629	unclassified	uncharacterized	Predicted gene; sparse annotation; likely follows cluster context.
Zfhx3	neuron	excitatory neuron	ATBF1 TF enriched in cortical/thalamo-cortical neurons.
Selplg	leukocyte	infiltrating monocyte	PSGL-1; adhesion receptor on blood-borne myeloid cells.
Srgap2	neuron	excitatory neuron	Spine morphogenesis regulator; neuronal development marker.
Atp8a2	neuron	projection neuron	Phospholipid flippase enriched in neurons/axons.
4933406I18Rik	unclassified	uncharacterized	Predicted transcript with uncertain brain specificity.
Ophn1	neuron	synaptic neuron	RhoGAP at dendritic spines; neuronal synaptic function.
Csmd3	neuron	excitatory neuron	Large adhesion protein enriched in cortical/hippocampal neurons.
Ltc4s	microglia	activated/eicosanoid	Leukotriene C4 synthase; arachidonic pathway in myeloid cells.
Crybb1	unclassified	likely contaminant	Lens β-crystallin; atypical in brain single cells.
Dock8	lymphocyte	T/B/NK cell	Immune cell cytoskeletal regulator; indicates peripheral lymphocytes.
P3h2	neuron	secretory/excitatory neuron	Prolyl-3-hydroxylase (LEPREL1); neuronal/olfactory enrichment.
Lrmda	unclassified	uncharacterized	Developmental gene; limited CNS cell-type data.
Fhit	unclassified	ubiquitous/unspecific	Broad tumor-suppressor gene with low cell-type specificity.

This set is microglia-leaning with both homeostatic (P2ry12, Siglech) and activated/eicosanoid programs (Ccr5, Lpcat2, Ltc4s). Several neuronal genes (Zfhx3, Srgap2, Atp8a2, Ophn1, Csmd3, P3h2) indicate a mixed signal or nearby neurons. Dock8 and Selplg point to rare infiltrating lympho-myeloid cells. Multiple predicted or nonspecific genes remain unassigned.

7.2.2.7 Cluster 6

Gene	Cell	Subtype	Notes
Rasip1	endothelial	capillary endothelial	Essential for endothelial junctions and lumen formation.
She	endothelial	signaling/adaptor	SH2 adaptor enriched in endothelial signaling contexts.
Ocln	endothelial	capillary endothelial	Tight-junction protein at BBB endothelium.
Kank3	endothelial	cytoskeletal/junctional	Cytoskeleton regulator reported in vascular endothelium.
Slc16a4	endothelial	transporter	Monocarboxylate transporter expressed in vascular endothelium.
Wfdc1	endothelial	secreted/glycoprotein	PS20; endothelial/perivascular secretion in brain.
Icam2	endothelial	capillary/venous	Classical endothelial adhesion molecule.
Ushbp1	endothelial	junctional scaffold	Tight-junction–associated adaptor in endothelial/epithelial cells.
Far2	oligodendrocyte	mature myelinating	Fatty acyl-CoA reductase; myelin/oligodendrocyte enriched.
Hspa12b	endothelial	stress-responsive	Endothelial-enriched HSP with vascular protection roles.
Thsd1	endothelial	tip/shear-responsive	Thrombospondin type-1 receptor; endothelial tip-cell marker.
Maoa	pericyte	vascular mural cell	MAO-A detected in mural cells and vascular compartments.
Igf1r	endothelial	capillary endothelial	IGF receptor present on brain endothelium.
Eogt	endothelial	secretory/O-GlcNAc	Glycosyltransferase modifying secreted proteins in endothelium.
Rgs12	pericyte	vascular mural cell	Regulator of G-protein signaling enriched in perivascular cells.
Slc30a1	endothelial	metal ion transport	Zn transporter detected in vascular endothelium.
Cav2	endothelial	caveolae-rich	Caveolin-2; abundant in endothelial caveolae.
Gpcpd1	endothelial	lipid metabolism	Glycerophosphocholine phosphodiesterase in vascular cells.
Hip1	endothelial	endocytic adaptor	Endocytosis/scaffold protein in endothelial trafficking.
Luzp1	endothelial	cytoskeletal	Actin-associated protein with vascular expression.

The profile is predominantly endothelial with strong junctional, caveolar, and transport signatures (Rasip1, Ocln, Icam2, Cav2, Hspa12b, Thsd1). Pericyte markers (Rgs12, Maoa) indicate mural cell admixture. Far2 suggests minor oligodendrocyte contamination. Overall, this cluster maps to brain microvascular endothelium with some perivascular support cells.

7.2.2.8 Cluster 7

Gene	Cell	Subtype	Notes
Tspan2	oligodendrocyte	mature/myelinating	Tetraspanin enriched in myelinating OLs and myelin membranes.
Pak1	neuron	excitatory neuron	p21-activated kinase; high in neurons for spine/actin signaling.
Ablim2	neuron	excitatory neuron	Actin-binding LIM protein enriched in CNS neurons/axons.
Ddr1	oligodendrocyte	mature/myelinating	Collagen receptor strongly expressed in OLs in brain atlases.
Sytl2	oligodendrocyte	vesicle/trafficking OL	Synaptotagmin-like protein detected in OL lineage; secretory trafficking.
Tmod1	neuron	excitatory neuron	Tropomodulin; actin capping at synapses/axons, neuronal enrichment.
Aatk	neuron	excitatory neuron	Neuronal kinase linked to neurite outgrowth and survival.
Sox10	oligodendrocyte	OL lineage TF	Master TF for OL/Schwann lineage and myelin gene program.
Serinc5	oligodendrocyte	lipid/myelin synthesis	Serine incorporator; supports sphingolipid/myelin lipid pathways in OLs.
Sh3gl3	neuron	synaptic neuron	Endophilin A3; clathrin-mediated endocytosis at synapses.
Tnni1	muscle cell	skeletal muscle (contaminant)	Slow skeletal troponin I; not typical for CNS parenchyma.
Lpar1	OPC	oligodendrocyte precursor	Canonical OPC receptor (LPA1) marking progenitors.
Tspan15	oligodendrocyte	mature/myelinating	Tetraspanin with OL-enriched expression in CNS datasets.
Cerox1	neuron	excitatory neuron (lncRNA)	Brain lncRNA modulating mitochondrial complex I; neuronal bias.
Usp54	unclassified	ubiquitous/unspecific	Deubiquitinase with broad expression; limited cell-type specificity.
Pou3f1	OPC	early differentiating OL	POU-domain TF (Oct6/Scip) in OL differentiation.
Lpgat1	oligodendrocyte	myelin lipid metabolism	Lysophospholipid acyltransferase; supports OL membrane biogenesis.
Gm10863	unclassified	uncharacterized	Predicted transcript; assignment unclear.
Neat1	astrocyte	protoplasmic astrocyte (lncRNA)	Paraspeckle lncRNA robust in glia, notably astrocytes.
Kit	mast cell	perivascular mast cell	c-Kit receptor; marks resident mast cells near CNS vasculature.

Most genes map to the oligodendrocyte lineage, mixing OPC markers (Lpar1, Pou3f1) with mature/myelinating programs (Tspan2, Ddr1, Serinc5, Tspan15, Lpgat1, Sox10). Several neuronal structural/vesicle genes (Pak1, Ablim2, Sh3gl3, Tmod1, Aatk, Cerox1) suggest nearby neurons or doublets. Neat1 indicates a glial/astrocytic component. Kit points to rare perivascular mast cells, and Tnni1 likely reflects ambient or non-CNS contamination.

7.2.2.9 Cluster 8

Gene	Cell	Subtype	Notes
Atf3	microglia	injury/stress-activated	Immediate-early TF induced by neuronal injury or inflammation in microglia.
Dusp1	microglia	MAPK feedback/activated	ERK phosphatase; rapid-response gene in activated myeloid cells.
Ptchd1	neuron	excitatory neuron	Patched domain-containing protein; enriched in cortical/hippocampal neurons.
Mylip	microglia	lipid metabolism	MYLIP/IDOL; regulates LDLR degradation in myeloid cells.
Runx1	microglia	developmental/reactive	TF in microglial development and in reactive states after injury.
Rgs2	microglia	GPCR signaling feedback	GPCR regulator; induced by cytokines in microglia.
Basp1	neuron	excitatory neuron	Axonal membrane protein enriched in neurons.
C3ar1	microglia	complement receptor	High in microglia during inflammation; binds C3a.
Mir142hg	microglia	inflammatory	Host gene for miR-142; myeloid-enriched under activation.
Mafb	microglia	transcriptional regulator	Maintains mature microglial identity and phagocytic function.
Abcd2	microglia	lipid transport	Peroxisomal transporter; enriched in microglia/oligodendrocytes.
Cd84	microglia	immune receptor	SLAM family; expressed in activated microglia.
Gm26542	unclassified	uncharacterized	Predicted transcript; limited annotation.
Ifitm10	microglia	IFN-response	IFN-induced transmembrane family member.
Creb5	microglia	transcription factor	CREB family TF induced in immune activation.
Gm35417	unclassified	uncharacterized	Predicted transcript; unknown specificity.
Cotl1	microglia	actin-binding	Myeloid actin-bundling protein linked to phagocytosis.
Ly86	microglia	co-receptor	MD-1; immune receptor accessory protein in myeloid cells.
H1f2	oligodendrocyte	immature/OPC	Histone H1 variant expressed in developing OLs.
Sgk1	microglia	stress/glucocorticoid-responsive	Serum/glucocorticoid-regulated kinase in stress-activated myeloid cells.

Cluster 8 is dominated by activation/stress-responsive microglia, with strong immediate-early (Atf3, Dusp1), immune receptor (C3ar1, Ly86, Cd84), lipid-handling (Mylip, Abcd2), and transcriptional (Runx1, Mafb, Creb5) programs. Several neuronal genes (Ptchd1, Basp1) likely reflect ambient or doublet signals. H1f2 indicates minor oligodendrocyte/OPC contamination. The overall profile suggests reactive microglia responding to injury, inflammation, or stress.

7.2.2.10 Cluster 9

Gene	Cell	Subtype	Notes
Anln	OPC	cycling OPC	Cytokinesis scaffold; marks proliferating progenitors.
Enpp6	oligodendrocyte	newly formed oligodendrocyte	Canonical NFOL marker during early differentiation.
Apod	oligodendrocyte	mature/supportive OL	Apolipoprotein D; glial lipid transport, enriched in OL/astroglia.
Ermn	oligodendrocyte	myelinating oligodendrocyte	Ermin; myelin cytoskeleton protein in OLs.
Trf	oligodendrocyte	mature myelinating	Transferrin secreted by OLs; iron handling for myelin.
Gjb1	oligodendrocyte	myelinating oligodendrocyte	Connexin32 in OLs and Schwann cells.
Serpinb1a	leukocyte	neutrophil/monocyte	Protease inhibitor typical of peripheral myeloid cells; rare in CNS parenchyma.
Septin8	oligodendrocyte	differentiating OL	Cytoskeletal GTPase implicated in OL maturation.
Acot7	neuron	excitatory neuron	Neuronal thioesterase; strong neuronal enrichment.
Pacs2	neuron	excitatory neuron	ER–mitochondria contact regulator; neuron-biased expression.
Klk6	oligodendrocyte	mature/reactive OL	Serine protease abundant in OLs and white matter.
Ppp2r2c	neuron	excitatory neuron	PP2A B55-γ regulatory subunit; brain/neuronal enriched.
Sccpdh	unclassified	ubiquitous enzyme	Saccharopine dehydrogenase; limited cell-type specificity.
Dip2a	neuron	excitatory neuron	Developmental receptor highly expressed in cortical neurons.
Eml2	unclassified	structural/microtubule	Broad expression; not cell-type specific in brain.
Usp31	unclassified	deubiquitinase	Sparse CNS specificity reported.
Inpp5f	oligodendrocyte	membrane/trafficking OL	Phosphoinositide 5-phosphatase with OL/neuronal enrichment.
Pdlim2	unclassified	cytoskeletal/NF-κB regulator	Broad regulator; cell-type assignment uncertain in CNS.
Plin3	oligodendrocyte	lipid-droplet OL	Perilipin-3; lipid storage/turnover in myelinating glia.
A530053G22Rik	unclassified	uncharacterized	Predicted gene; assignment unclear.

The set is dominated by oligodendrocyte lineage, especially newly formed and myelinating states (Enpp6, Ermn, Trf, Gjb1, Klk6, Plin3). One marker indicates proliferating OPCs (Anln). Several neuronal genes appear as minor admixture (Acot7, Pacs2, Ppp2r2c, Dip2a). Serpinb1a suggests rare peripheral myeloid contamination. Multiple genes are nonspecific or uncharacterized.

7.2.2.11 Cluster 10

Gene	Cell	Subtype	Notes
Slc6a11	astrocyte	protoplasmic astrocyte	GAT-3; astrocytic GABA uptake at synapses.
Agt	astrocyte	protoplasmic astrocyte	Angiotensinogen produced by astrocytes in CNS.
Atp13a4	astrocyte	reactive/secretory astrocyte	P-type ATPase enriched in astroglia; stress-responsive.
Spon1	neuron	excitatory neuron	F-spondin; axon guidance protein in cortical/thalamo-cortical neurons.
Lgi1	neuron	excitatory neuron	Secreted synaptic organizer for AMPA signaling; neuron-specific.
Itih3	astrocyte	ECM/HA-interacting astrocyte	Matrisomal protein linked to astrocyte ECM.
Gpld1	astrocyte	secreted astrocyte	GPI-anchored protein cleavage; detected in astrocyte secretome.
Fads2	oligodendrocyte	myelinating oligodendrocyte	Fatty acid desaturase supporting myelin lipid synthesis.
Kank1	astrocyte	cytoskeletal astrocyte	Actin–microtubule linker expressed in astrocytes.
B230323A14Rik	unclassified	uncharacterized	Predicted transcript; cell-type bias unclear.
Sfrp5	astrocyte	Wnt-modulatory astrocyte	Secreted Wnt antagonist detected in astroglia.
Slc6a1	neuron	inhibitory neuron (GABAergic)	GAT-1; presynaptic GABA transporter in interneurons.
Abat	astrocyte	metabolic astrocyte	GABA transaminase for astrocytic GABA catabolism.
Camk2g	neuron	excitatory neuron	CAMK2 isoform enriched in pyramidal neurons.
Fam228b	unclassified	uncharacterized	Limited CNS annotation.
Cyp2j6	endothelial	brain endothelium	CYP epoxygenase expressed in cerebrovascular endothelium.
Rgma	oligodendrocyte	myelin-associated inhibitor	RGMa limits axon growth; expressed in OLs and myelin.
Phka1	neuron	excitatory neuron	Phosphorylase kinase α1; neuronal energy metabolism.
Pitpnc1	neuron	excitatory neuron	PI transfer protein at synapses; neuron-enriched.
Sparc	astrocyte	perivascular/ECM astrocyte	Secreted matricellular protein from astrocytes and glia limitans.

This set centers on astrocytes with GABA handling and ECM programs (Slc6a11, Agt, Itih3, Gpld1, Sfrp5, Sparc, Abat). Neuronal markers define excitatory and inhibitory components (Lgi1, Camk2g, Slc6a1, Pitpnc1, Spon1). Oligodendrocyte and myelin-related genes appear (Fads2, Rgma). One endothelial xenobiotic enzyme suggests a vascular signal (Cyp2j6). Several entries remain uncharacterized.

7.2.2.12 Cluster 11

Gene	Cell	Subtype	Notes
Gldc	astrocyte	metabolic astrocyte	Glycine cleavage enzyme enriched in astrocytic metabolism.
Cspg5	neuron	excitatory neuron	Neuroglycan C; neuronal membrane proteoglycan at synapses.
Fjx1	neuron	excitatory neuron	Developmental signaling protein with neuronal enrichment.
Gli3	astrocyte	radial glia–like astrocyte	Patterning TF retained in astroglial lineages.
Scrg1	astrocyte	reactive/secretory astrocyte	Secreted protein up in glia during stress and remodeling.
Grin2c	neuron	excitatory neuron (thalamic/cerebellar bias)	NMDA receptor NR2C subunit in thalamus and granule neurons.
St6galnac5	endothelial	brain endothelium	BBB-enriched sialyltransferase in CNS endothelium.
4930488L21Rik	unclassified	uncharacterized	Predicted transcript; cell-type bias unclear.
Prdx6	astrocyte	antioxidant astrocyte	Peroxiredoxin-6; glial ROS defense.
Mfge8	astrocyte	perivascular/ phagocytosis-support	Astrocyte-derived opsonin promoting debris clearance.
Tspan7	neuron	excitatory neuron	Synaptic tetraspanin; neuronal dendrite/spine expression.
Pantr1	endothelial	tip-cell–like endothelium	lncRNA linked to angiogenic endothelial programs.
Msi2	astrocyte	progenitor-like astrocyte	Neural stem/astroglial RNA-binding protein.
Hopx	astrocyte	protoplasmic astrocyte	Marker of cortical/hippocampal astrocyte lineages.
Ckb	neuron	excitatory neuron	Creatine kinase B; high neuronal energy enzyme.
Mgll	neuron	excitatory neuron	Synaptic monoacylglycerol lipase enriched in neurons.
Gstm5	astrocyte	detox/oxidative-stress astrocyte	GST isoform enriched in glia for xenobiotic defense.
Garem1	neuron	excitatory neuron	MAPK pathway adaptor with neuronal enrichment.
Gfap	astrocyte	protoplasmic astrocyte	Canonical intermediate filament of astrocytes.

The profile centers on astrocytes, including protoplasmic and progenitor-like states (Gfap, Hopx, Msi2, Prdx6, Mfge8). Neuronal synaptic and metabolic genes form a secondary component (Tspan7, Grin2c, Ckb, Mgll, Cspg5). Endothelial signals appear via St6galnac5 and Pantr1. Overall, cluster 11 most likely represents astrocytes with minor neuronal and vascular admixture.

7.2.2.13 Cluster 12

Gene	Cell	Subtype	Notes
Lgals3	microglia	DAM/activated	Galectin-3; high in phagocytic, injury-responsive microglia.
Ms4a7	microglia	activated/monocyte-like	MS4A7 up in inflammatory microglia and infiltrating myeloid cells.
Ftl1	microglia	iron-handling	Ferritin light chain; iron sequestration in activated microglia.
Cd68	microglia	phagocytic	Lysosomal glycoprotein marking phagocytes.
C3ar1	microglia	complement receptor	C3a receptor; elevated with inflammation.
Cd72	B cell	B cell	BCR co-receptor; indicates infiltrating B lineage.
Glipr1	microglia	activated	p53-responsive myeloid protein increased by inflammatory cues.
Itga5	microglia	adhesion/activated	Fibronectin receptor α5; rises in reactive myeloid cells.
Cacna1a	neuron	excitatory neuron	P/Q-type Ca²⁺ channel (CaV2.1) in glutamatergic neurons.
Ell2	plasma cell	antibody-secreting cell	Transcription elongation factor driving Ig production in plasma cells.
Fth1	microglia	iron-handling	Ferritin heavy chain; oxidative/iron stress in microglia.
Arhgap22	microglia	cytoskeletal/activated	RhoGAP regulating myeloid motility; LPS-inducible.
Mmp12	microglia	activated/macrophage-like	Macrophage elastase; up in reactive microglia.
Hectd2os	unclassified	uncharacterized	Antisense lncRNA; unclear brain cell-type bias.
Lonrf3	neuron	excitatory neuron	Neuron-enriched E3 ligase family member in CNS.
Lyz2	microglia	activated	Lysozyme; hallmark myeloid enzyme.
Pfkfb3	microglia	glycolytic/activated	Glycolysis driver induced in inflammatory microglia.
Fabp5	microglia	lipid-handling/DAM	Fatty acid–binding protein in lipid-laden microglia.
Ch25h	microglia	IFN/lipid program	Cholesterol 25-hydroxylase; antiviral and lipid pathways in microglia.
Apoc1	microglia	DAM/lipid	ApoC1; strong in Trem2⁺ lipid-processing microglia.

This set maps chiefly to activated/DAM microglia with phagocytic, lipid, iron, and glycolytic programs (Lgals3, Ms4a7, Cd68, C3ar1, Fabp5, Apoc1, Ftl1/Fth1, Pfkfb3). Mmp12 and Lyz2 reinforce a macrophage-like state. Cacna1a and Lonrf3 suggest minor neuronal admixture. Cd72 and Ell2 indicate a small B/plasma cell presence. Hectd2os remains unassigned.

7.2.2.14 Cluster 13

Gene	Cell	Subtype	Notes
Fgf13	neuron	excitatory neuron	Intracellular FGFs; high in axons/dendrites of CNS neurons.
Plxdc2	endothelial	tip-cell/angiogenic endothelial	Plexin domain–containing protein in brain endothelium.
Apbb1ip	microglia	immune/cytoskeletal	RIAM adaptor in integrin signaling; present in myeloid cells.
Lrmda	unclassified	uncharacterized	Developmental gene; uncertain CNS cell-type bias.
Cacna1a	neuron	excitatory neuron	P/Q-type Ca²⁺ channel in glutamatergic neurons.
Nrp1	endothelial	tip-cell/angiogenic endothelial	Neuropilin-1; VEGF receptor cofactor in CNS vasculature.
Arhgap24	endothelial	vascular cytoskeleton	RhoGAP regulating endothelial junctions and sprouting.
Mir99ahg	endothelial	angiogenic lncRNA	Host gene for miR-99a; expressed in endothelial cells.
Gm15155	unclassified	uncharacterized	Predicted transcript; unclear assignment.
Fyb	microglia	immune adaptor	Fyn-binding protein; immune cell signaling, myeloid enriched.
Tanc2	neuron	excitatory neuron	Postsynaptic scaffold in excitatory synapses.
Cx3cr1	microglia	homeostatic microglia	Fractalkine receptor; canonical resident microglial marker.
4933406I18Rik	unclassified	uncharacterized	Predicted gene; unknown specificity.
Nav2	neuron	excitatory neuron	Neuron navigator protein; axonal guidance.
Hpgds	microglia	lipid/eicosanoid	Hematopoietic PGD synthase in myeloid cells.
Gpr34	microglia	homeostatic/anti-inflammatory	P2Y-like GPCR enriched in microglia.
Mamdc2	endothelial	vascular ECM	Secreted adhesion molecule from CNS endothelium.
Sdk1	neuron	excitatory neuron	Synaptic cell adhesion molecule in cortical neurons.
Wwox	neuron	excitatory neuron	Tumor suppressor; neuronal dendrite maintenance.
Plcl1	neuron	excitatory neuron	Phospholipase C–like protein; neuronal signal transduction.

Cluster 13 shows a mixed neuronal–endothelial–microglial profile. Neuronal structural/signaling genes (Fgf13, Cacna1a, Tanc2, Nav2, Sdk1, Wwox, Plcl1) dominate. Endothelial angiogenic/junctional markers (Plxdc2, Nrp1, Arhgap24, Mir99ahg, Mamdc2) suggest strong vascular contribution. Microglial homeostatic and lipid-handling markers (Cx3cr1, Gpr34, Hpgds, Fyb) indicate perivascular or vessel-associated microglia. The composition points to neurovascular interface cells.

7.2.2.15 Cluster 14

Gene	Cell	Subtype	Notes
Ifi211	microglia	interferon-responsive	Ifi200 family ISG induced by type I IFN in myeloid cells.
Mx1	microglia	interferon-responsive	Dynamin-like antiviral GTPase; classic ISG in microglia.
Ifit3	microglia	interferon-responsive	ISG that binds viral RNA; elevated in activated microglia.
Ifit2	microglia	interferon-responsive	Antiviral ISG; robust in myeloid IFN programs.
A330040F15Rik	unclassified	uncharacterized	Predicted transcript; often co-expressed with ISG modules.
Ifi207	microglia	interferon-responsive	Ifi200 family ISG; myeloid-biased induction.
Rsad2	microglia	interferon-responsive (viperin)	Antiviral enzyme; strong in IFN-stimulated microglia.
Oasl2	microglia	interferon-responsive	2′–5′-oligoadenylate synthase-like ISG in myeloid cells.
Ifi204	microglia	interferon-responsive	PYHIN DNA-sensor family; induced in myeloid IFN states.
Gm4951	unclassified	uncharacterized	Predicted gene; tracks with ISG clusters.
Ccl12	microglia	inflammatory chemokine	Monocyte-recruiting chemokine produced by activated myeloid cells.
Rnf213	endothelial	interferon-responsive endothelium	Moyamoya-linked E3 ligase; enriched in IFN-activated endothelium.
Parp14	microglia	interferon/STAT-linked	ADP-ribosyltransferase up in IFN/STAT signaling.
Herc6	microglia	interferon-responsive	ISG15 E3 ligase; part of antiviral ISGylation pathway.
Ifih1	microglia	RNA-sensing/IFN	MDA5 cytosolic sensor driving type I IFN responses.
Bst2	microglia	interferon-responsive	Tetherin; classic ISG induced in activated microglia.
Pik3ap1	microglia	immune-signaling adaptor	BCAP adaptor; TLR/BCR pathway component in myeloid cells.
Cxcl10	microglia	interferon-induced chemokine	IP-10; produced by IFN-stimulated microglia/astroglia; choose microglia here.
Lyn	microglia	Src-family kinase	Immune kinase functioning in myeloid receptor signaling.
Slc15a3	microglia	lysosomal/IFN-linked	Endolysosomal peptide transporter enriched in activated myeloid cells.

This set defines a strong interferon-stimulated program in microglia, including core ISGs (Mx1, Ifit2/3, Rsad2, Oasl2, Ifi20x family) plus IFN-induced chemokines (Cxcl10, Ccl12) and immune signaling nodes (Ifih1, Lyn, Pik3ap1, Slc15a3). Rnf213 points to a concurrent interferon signature in brain endothelium. Two predicted genes co-track with the ISG module. Overall, the cluster represents IFN-activated microglia with minor endothelial ISG input.

7.2.2.16 Cluster 15

Gene	Cell	Subtype	Notes
Itk	T cell	CD8⁺/CD4⁺ T lymphocyte	Tec family kinase critical for TCR signaling.
Cd3g	T cell	CD8⁺/CD4⁺ T lymphocyte	CD3 complex component; pan-T-cell marker.
Cd3e	T cell	CD8⁺/CD4⁺ T lymphocyte	CD3 complex epsilon chain; pan-T-cell marker.
Grap2	T cell	CD8⁺/CD4⁺ T lymphocyte	Adaptor in TCR signaling; lymphoid-specific.
Cxcr6	T cell	tissue-resident memory T cell	Chemokine receptor marking TRM cells in tissues including CNS.
Themis	T cell	CD4⁺/CD8⁺ T lymphocyte	Thymocyte selection-associated protein; T-cell signaling.
Gimap4	T cell	CD4⁺/CD8⁺ T lymphocyte	GTPase enriched in peripheral T cells.
Lck	T cell	CD4⁺/CD8⁺ T lymphocyte	Src-family kinase essential for TCR signal transduction.
Trac	T cell	CD4⁺/CD8⁺ T lymphocyte	TCR alpha chain constant region; pan-T marker.
Stat4	T cell	Th1-polarized T cell	TF driving IFN-γ–producing Th1 and Tc1 programs.
Cd226	T cell	activated T cell	DNAM-1 adhesion receptor; up in cytotoxic/activated T cells.
Ikzf3	T cell	CD4⁺/CD8⁺ T lymphocyte	Aiolos TF; lymphoid cell development.
Ctsw	T cell	cytotoxic T cell	Granule-associated cathepsin in cytotoxic lymphocytes.
Runx3	T cell	CD8⁺ cytotoxic T cell	TF driving cytotoxic lineage and effector functions.
Cd8b1	T cell	CD8⁺ cytotoxic T cell	CD8 β chain; hallmark of cytotoxic T cells.
Adam19	unclassified	broad	Metalloprotease; not T-specific, may be expressed in multiple cell types.
Pde7a	T cell	CD4⁺/CD8⁺ T lymphocyte	cAMP-specific phosphodiesterase enriched in T cells.
Gramd3	unclassified	broad/immune	GRAM domain protein with immune enrichment but low specificity.
Bcl2	T cell	memory T cell	Anti-apoptotic factor enriched in long-lived T cells.
Ptprc	leukocyte	pan-leukocyte	CD45; expressed in all hematopoietic cells.

This set is a classic T-cell transcriptional program, with core TCR components (Cd3e, Cd3g, Trac, Lck), signaling/adaptor molecules (Itk, Grap2, Themis), lineage-defining TFs (Runx3, Stat4, Ikzf3), and cytotoxic effectors (Ctsw, Cd8b1). Cxcr6 and Bcl2 suggest tissue-resident memory and long-lived subsets. Ptprc confirms hematopoietic origin. Non-specific genes (Adam19, Gramd3) are likely background or broadly expressed immune genes. Overall, the cluster represents predominantly CD8⁺ tissue-resident/effector T cells infiltrating brain tissue.

7.2.2.17 Cluster 16

Gene	Cell	Subtype	Notes
Calml4	ependymal	motile ciliated ependymal cell	Calmodulin-like protein enriched in ciliated ventricular cells.
Drc7	ependymal	motile ciliated ependymal cell	Dynein regulatory complex protein; key for ciliary motility.
Ecrg4	ependymal	secretory ependymal cell	Cerebral spinal fluid–associated secreted protein from choroid plexus/ependymal cells.
2900040C04Rik	unclassified	uncharacterized	Predicted gene; expression context unclear but may align with ependymal profile.
Rsph1	ependymal	motile ciliated ependymal cell	Radial spoke head protein; ciliary motility.
Prr32	unclassified	uncharacterized	Predicted protein; cell-type bias unclear.
Clic6	ependymal	choroid plexus epithelium	Chloride channel enriched in CSF-producing epithelium.
Kl	ependymal	choroid plexus epithelium	Klotho; secreted protein from choroid plexus/ependymal cells.
Ppp1r1b	neuron	dopaminoceptive neuron	DARPP-32; medium spiny neurons in striatum.
Rbp1	ependymal	choroid plexus/retinoid handling	Retinol-binding protein in CSF-secreting cells.
Gsta4	unclassified	antioxidant enzyme	Glutathione S-transferase; expressed in multiple CNS cell types.
Cdkn1c	ependymal	choroid plexus/ependymal	Cell cycle inhibitor in epithelial/ependymal cells.
Cfap126	ependymal	motile ciliated ependymal cell	Cilia-associated protein.
Pcp4	neuron	calmodulin-binding neuron	Purkinje cell protein 4; neuronal calcium signaling.
Chchd10	neuron	excitatory neuron	Mitochondrial protein enriched in neurons.
Ezr	ependymal	apical junctional protein	Ezrin in epithelial/ependymal microvilli.
Stk39	unclassified	broad	Kinase with expression in multiple CNS cell types.
Ttr	ependymal	choroid plexus epithelium	Transthyretin; hallmark secreted protein from choroid plexus.
Fabp3	neuron	excitatory neuron	Heart-type fatty acid–binding protein enriched in neurons.
Cd59a	endothelial	vascular endothelium	Complement regulatory protein in CNS vasculature.

Cluster 16 is dominated by ependymal/choroid plexus epithelial markers, including motile cilia components (Drc7, Rsph1, Cfap126), secretory/transport proteins (Ttr, Kl, Clic6, Rbp1), and apical structural proteins (Ezr, Cdkn1c). A few neuronal genes (Ppp1r1b, Pcp4, Chchd10, Fabp3) suggest minor neuronal contamination, while Cd59a points to vascular contact. Overall, the profile matches motile ciliated and secretory ependymal cells of the ventricular and choroid plexus lining.

7.2.2.18 Cluster 17

Gene	Cell	Subtype	Notes
Rbfox3	neuron	pan-neuronal	NeuN; canonical neuronal nuclear marker.
Ryr2	neuron	excitatory projection neuron	Ryanodine receptor; high in glutamatergic projection neurons.
Grin2a	neuron	excitatory neuron	NMDA receptor NR2A subunit enriched in cortical/hippocampal neurons.
Kcnip4	neuron	excitatory neuron	Kv channel–interacting protein enriched in pyramidal neurons.
Gabrb2	neuron	inhibitory synapse–receiving neuron	GABA\(_A\) β2 subunit; broad neuronal, postsynaptic to GABA input.
Grm1	neuron	excitatory/metabotropic	mGluR1; strong in cerebellar Purkinje and some forebrain excitatory neurons.
Fam135b	neuron	excitatory neuron (putative)	Neuron-enriched transcript; limited cell-type specificity.
Pde10a	neuron	striatal medium spiny neuron	cAMP/cGMP PDE highly expressed in MSNs.
Cnksr2	neuron	excitatory synaptic scaffold	Postsynaptic scaffold at glutamatergic synapses.
Vsnl1	neuron	excitatory neuron	Neuronal Ca\(^{2+}\) sensor enriched in projection neurons.
Pcsk2	neuron	neurosecretory neuron	Prohormone convertase in peptidergic neurons.
Slit3	neuron	developing/axonal guidance	Axon guidance cue expressed in neurons.
Sphkap	neuron	excitatory neuron	PKA-anchoring protein enriched in neurons.
Celf2	neuron	excitatory neuron	RNA-binding/splicing factor prominent in neurons.
A230006K03Rik	unclassified	uncharacterized	Predicted gene; neuronal-biased in atlases but not definitive.
Chgb	neuron	neurosecretory neuron	Chromogranin B; dense-core vesicle protein in neurons.
Lingo2	neuron	excitatory neuron	Leucine-rich repeat protein in CNS neurons.
Sncb	neuron	pan-neuronal	β-synuclein; presynaptic neuronal protein.
Nell1	neuron	developing excitatory neuron	Secreted EGF-like protein in neuronal development.
Ahi1	neuron	excitatory neuron	Jouberin; cilium/axon protein enriched in CNS neurons.

This set is neuron-dominant, with strong excitatory projection signatures (Grin2a, Kcnip4, Vsnl1, Cnksr2, Sphkap) and neurosecretory markers (Pcsk2, Chgb). Pde10a points to a striatal MSN subset. Grm1 suggests some cerebellar/forebrain excitatory contribution. One broad GABA\(_A\) receptor subunit (Gabrb2) reflects inhibitory synaptic input rather than interneuron identity. Overall, the cluster maps to excitatory projection neurons with a striatal component.

7.2.2.19 Cluster 19

Gene	Cell	Subtype	Notes
Slc38a11	pericyte	capillary pericyte	Amino acid transporter reported in perivascular/mural cells.
Slc6a20a	endothelial	venous/capillary endothelium	SIT1 transporter detected at the BBB endothelium.
Atp13a5	pericyte	mural/pericyte	P-type ATPase enriched in brain pericytes.
Pdgfrb	pericyte	capillary pericyte	Canonical pericyte receptor tyrosine kinase.
Vtn	perivascular fibroblast	vascular fibroblast	Vitronectin; ECM protein from perivascular fibroblasts.
Notch3	smooth muscle	arteriolar SMC	Receptor defining arteriolar smooth muscle and some pericytes.
Abcc9	pericyte	mural/pericyte	K\(_\text{ATP}\) channel SUR2; high in pericytes/SMC.
Gjc1	smooth muscle	vascular SMC/pericyte	Connexin45 in mural gap junctions.
Tbx3os1	unclassified	mural-associated lncRNA	Antisense to Tbx3; reported near vascular smooth muscle programs.
Higd1b	endothelial	capillary/tip-like	Hypoxia-inducible mitochondrial protein in endothelium.
Aspn	perivascular fibroblast	vascular fibroblast	Asporin; matrix component of perivascular fibroblasts.
Sod3	endothelial	perivascular/endothelial	Extracellular superoxide dismutase secreted by endothelium.
Mgp	smooth muscle	vascular SMC/pericyte	Matrix Gla protein abundant in mural cells; anti-calcification.
Ackr3	endothelial	venous/angiogenic endothelium	Atypical chemokine receptor CXCR7 on CNS endothelium.
Dlc1	endothelial	junction/cytoskeleton	RhoGAP regulating endothelial junctions and sprouting.
Cald1	smooth muscle	vascular SMC	Caldesmon; contractile apparatus component.
Edn1	endothelial	endothelial (peptide hormone)	Endothelin-1; secreted by endothelium to signal mural cells.
Myh11	smooth muscle	vascular SMC	Smooth muscle myosin heavy chain; hallmark SMC marker.
Tagln	smooth muscle	vascular SMC	SM22α; classic SMC contractile marker.
Dcn	perivascular fibroblast	vascular fibroblast	Decorin; ECM proteoglycan from perivascular fibroblasts.

This set maps to the neurovascular unit with dominance of mural cells. Pericyte and SMC markers (Pdgfrb, Abcc9, Notch3, Myh11, Tagln, Cald1, Mgp, Gjc1) define a pericyte–smooth muscle program. Multiple endothelial genes (Slc6a20a, Higd1b, Ackr3, Dlc1, Edn1, Sod3) indicate close endothelial association. ECM genes (Vtn, Dcn, Aspn) support a perivascular fibroblast component. Overall, the cluster represents capillary/arteriolar mural cells with endothelial and fibroblast admixture.

7.2.2.20 Cluster 20

Gene	Cell	Subtype	Notes
Dcx	neuron	immature/developing neuron	Doublecortin; hallmark of migrating/immature neurons.
Dlx6os1	neuron	developing inhibitory neuron	Long non-coding RNA co-expressed with Dlx genes in GABAergic precursors.
Igfbpl1	neuron	developing neuron	IGF-binding protein–like 1; enriched in maturing neurons.
Dlx1	neuron	developing inhibitory neuron	TF driving GABAergic interneuron development.
Sp9	neuron	developing inhibitory neuron	TF in striatal and cortical GABAergic interneuron differentiation.
Sox11	neuron	immature/developing neuron	TF promoting neuronal differentiation and neurite growth.
Kcnb2	neuron	excitatory neuron	Voltage-gated K\(^+\) channel in cortical/hippocampal pyramidal neurons.
Grip1	neuron	excitatory neuron	AMPA receptor trafficking protein; enriched in glutamatergic neurons.
Sdk2	neuron	excitatory neuron	Synaptic cell adhesion molecule in specific glutamatergic subsets.
Tenm4	neuron	excitatory neuron	Teneurin family adhesion/signaling protein in projection neurons.
Runx1t1	neuron	developing neuron	TF expressed during early neuronal maturation.
Mpped2	neuron	developing neuron	Metallophosphoesterase enriched in differentiating neurons.
Pbx3	neuron	developing neuron	TALE homeodomain TF in neuronal differentiation.
Epha6	neuron	excitatory neuron	Eph receptor in axonal guidance of cortical/hippocampal neurons.
Syn3	neuron	excitatory neuron	Synapsin III; vesicle trafficking in developing neurons.
Gm20754	unclassified	uncharacterized	Predicted transcript; co-expressed with neuronal programs.
Dync1i1	neuron	developing neuron	Dynein intermediate chain; axonal transport in immature neurons.
Hmgb3	neuron	developing neuron	Chromatin protein enriched in neural precursors.
Arx	neuron	developing inhibitory neuron	TF essential for forebrain GABAergic interneuron specification.
Dlx2	neuron	developing inhibitory neuron	TF for GABAergic interneuron migration/differentiation.

Cluster 20 strongly reflects immature/developing neurons, with a mixed but prominent GABAergic interneuron developmental program (Dlx1, Dlx2, Arx, Sp9, Dlx6os1) and generic neuronal maturation genes (Dcx, Sox11, Pbx3, Runx1t1, Mpped2). Several excitatory neuron markers (Kcnb2, Grip1, Sdk2, Tenm4, Epha6) indicate a minor glutamatergic component or transitional states. Overall, it likely represents developing GABAergic interneurons with some excitatory neuron admixture.

7.2.2.21 Cluster 22

Gene	Cell	Subtype	Notes
Mrc1	macrophage	perivascular (BAM, M2-like)	CD206; hallmark of perivascular/alternatively activated macrophages.
F13a1	macrophage	perivascular	Coagulation factor XIII A; high in tissue macrophages including BAMs.
Ms4a6c	macrophage	perivascular	MS4A family membrane protein enriched in macrophages.
Pid1	macrophage	perivascular	Endocytic/adaptor; myeloid-expressed, low specificity.
Pf4	macrophage	perivascular	Platelet factor 4 also expressed in BAM-like vascular macrophages.
Dab2	macrophage	perivascular/scavenging	Endocytic adaptor up in M2-like macrophages.
Cd163	macrophage	perivascular (hemoglobin-scavenging)	Canonical BAM marker; Hb–haptoglobin receptor.
Cd209f	macrophage	dendritic-like BAM	DC-SIGN family; myeloid antigen-capture at vessel interfaces.
Stab1	macrophage	perivascular/scavenger	Stabilin-1; M2-like macrophage scavenger receptor.
Iqgap1	macrophage	perivascular	Cytoskeletal scaffold in motile/adhesive myeloid cells.
Rnf150	macrophage	perivascular	RING E3; myeloid-enriched, low specificity.
Ifitm2	macrophage	interferon-responsive BAM	IFN-induced transmembrane protein in myeloid cells.
Maf	macrophage	M2-like transcriptional program	TF promoting alternative activation and tissue residency.
Slc9a9	macrophage	endolysosomal	NHE9; endosomal pH regulator in immune cells.
Ccl8	macrophage	chemokine-secreting	Monocyte-recruiting chemokine from activated macrophages.
Cebpb	macrophage	differentiation/activation	TF guiding macrophage inflammatory/M2 programs.
Fcgr2b	macrophage	inhibitory Fc receptor	ITIM-bearing FcγRIIb dampens activation in tissue macrophages.
Tsc22d3	macrophage	glucocorticoid-responsive (GILZ)	Anti-inflammatory regulator induced by steroids in macrophages.
Cytip	macrophage	adhesion/trafficking	Regulates integrin-mediated adhesion in leukocytes.
Srgn	macrophage	secretory granule core	Serglycin; granule proteoglycan in myeloid cells.

The gene set defines perivascular/border-associated macrophages with an M2-like, scavenging, and anti-inflammatory profile (Mrc1, Cd163, Stab1, Maf, Tsc22d3, Fcgr2b), plus chemokine and endolysosomal programs (Ccl8, Slc9a9, Srgn). Pf4 and Cd209f support a vascular-interface, antigen-capture phenotype. Low-specificity adaptors (Pid1, Iqgap1, Rnf150) fit within a macrophage context. Overall, this cluster maps to Mrc1⁺Cd163⁺ BAMs rather than parenchymal microglia.

7.2.2.22 Cluster 23

Gene	Cell	Subtype	Notes
Ndufa4l2	pericyte	hypoxia-responsive pericyte	HIF-inducible mitochondrial subunit; high in pericytes.
Egflam	perivascular fibroblast	vascular fibroblast	ECM/adhesion protein around vessels and meninges.
Il34	astrocyte	perivascular astrocyte	CSF1R ligand from astrocytes that supports microglia.
Gucy1b1	smooth muscle	arteriolar SMC	sGC β1 for NO signaling in mural cells.
Trpc3	smooth muscle	arteriolar SMC	Ca²⁺-permeable channel in vascular contractile cells.
Arhgap42	smooth muscle	arteriolar SMC	RhoGAP controlling vascular tone and junctions.
Art3	endothelial	capillary/venous endothelium	ADP-ribosyltransferase reported in vascular endothelium.
Lin7a	neuron	excitatory neuron	Synaptic scaffold; likely minor neuronal admixture.
Ctdspl	neuron	excitatory neuron	CTDSP family phosphatase; neuronal bias; likely admixture.
Galnt17	perivascular fibroblast	vascular fibroblast	O-glycosyltransferase enriched in perivascular stromal cells.
P2ry14	perivascular fibroblast	vascular fibroblast	UDP-sugar GPCR common in fibroblast/perivascular stromal cells.
Ecm2	perivascular fibroblast	vascular fibroblast	Matrix protein secreted by perivascular fibroblasts.
Sntb1	pericyte	contractile pericyte	Dystrophin-associated scaffold at vascular membranes.
Nbl1	perivascular fibroblast	vascular fibroblast	DAN family BMP modulator in vessel-adjacent stroma.
Airn	endothelial	vascular lncRNA	Imprinted lncRNA detected in vascular/endothelial niches.
Septin11	pericyte	contractile pericyte	Cytoskeletal GTPase in mural cells.
Kcnj8	pericyte	KATP pericyte	Kir6.1 partner of ABCC9 in pericytes/SMC.
Cspg4	pericyte	NG2⁺ pericyte	NG2 proteoglycan; classic marker of pericytes (also OPCs).
Ddit4l	pericyte	stress/hypoxia pericyte	REDD2; mTOR/HIF stress gene in mural cells.
Morrbid	macrophage	perivascular macrophage	Myeloid lncRNA; suggests minor BAM contamination.

The set maps to the neurovascular unit, dominated by pericytes and arteriolar smooth muscle (Kcnj8, Gucy1b1, Arhgap42, Septin11, Sntb1, Ndufa4l2) with a strong perivascular fibroblast ECM/GPCR signature (Ecm2, P2ry14, Galnt17, Nbl1, Egflam). Endothelial inputs appear via Art3 and Airn. Il34 points to perivascular astrocyte support. Neuronal genes (Lin7a, Ctdspl) likely reflect admixture. Overall, this cluster represents vessel-associated cells, centered on NG2⁺ pericytes and vascular fibroblasts.

7.2.2.23 Cluster 24

Gene	Cell	Subtype	Notes
Cfap141	ependymal	motile ciliated ependymal cell	Cilia- and flagella-associated protein in ventricular ependyma.
Cfap46	ependymal	motile ciliated ependymal cell	Ciliary motility protein in multiciliated CNS cells.
Lrrc23	ependymal	motile ciliated ependymal cell	Axonemal protein in multiciliated cells.
Ccdc170	ependymal	motile ciliated ependymal cell	Coiled-coil protein linked to ciliary structure.
Fam166c	ependymal	motile ciliated ependymal cell	Cilia-associated protein in multiciliated epithelia.
Foxj1	ependymal	motile ciliated ependymal cell	Master TF for motile ciliogenesis in ependymal cells.
Cfap206	ependymal	motile ciliated ependymal cell	Axonemal component in motile cilia.
Gm867	unclassified	uncharacterized	Predicted transcript; likely co-expressed in ciliated cells.
Odf3b	ependymal	motile ciliated ependymal cell	Outer dense fiber protein in cilia/flagella.
Sntn	ependymal	motile ciliated ependymal cell	Sentan; ciliary basal-plate component.
Dthd1	unclassified	uncharacterized	Death-domain protein; unclear CNS specificity.
Lrrc36	ependymal	motile ciliated ependymal cell	Leucine-rich repeat protein localized to cilia.
Fam166b	ependymal	motile ciliated ependymal cell	Ciliary protein enriched in multiciliated epithelia.
Frmpd2	ependymal	motile ciliated ependymal cell	FERM domain protein localized at apical ciliary membrane.
Cdhr4	ependymal	motile ciliated ependymal cell	Cadherin-related ciliary adhesion molecule.
1700024G13Rik	unclassified	uncharacterized	Predicted gene; likely co-expressed in ciliated epithelium.
1700016K19Rik	unclassified	uncharacterized	Predicted gene; likely associated with ciliated cell program.
Unc5cl	unclassified	axon guidance–related	Netrin receptor family; neuronal expression in other contexts, possibly minor contamination.
Dnah3	ependymal	motile ciliated ependymal cell	Dynein heavy chain in motile cilia.
Stoml3	neuron	sensory neuron	Mechanotransduction protein; likely ambient neuronal transcript.

Cluster 24 is overwhelmingly composed of motile cilia–associated proteins (Foxj1, Cfap family, Odf3b, Sntn, Dnah3) defining ventricular ependymal cells and choroid plexus multiciliated epithelium. Minor neuronal transcripts (Unc5cl, Stoml3) likely reflect contamination. Several predicted genes co-track with the ciliary module. Overall, this is a classic motile ciliated ependymal cell signature.

7.2.2.24 Cluster 25

Gene	Cell	Subtype	Notes
Sema3d	OPC	developing OPC	Axon guidance molecule expressed in oligodendrocyte precursors.
Cacng4	neuron	excitatory neuron	AMPA receptor auxiliary subunit; enriched in glutamatergic neurons.
Nxph1	neuron	excitatory neuron	Neurexophilin; synaptic ligand for neurexins in projection neurons.
Pdgfra	OPC	canonical OPC	Platelet-derived growth factor receptor α; hallmark OPC marker.
Ppfibp1	OPC	cytoskeletal/trafficking OPC	Liprin-β1; scaffolding in OL lineage cells.
Epn2	OPC	endocytic OPC	Epsin-2; endocytosis adaptor enriched in OPCs.
Adam12	OPC	proliferating OPC	Metalloprotease upregulated in developing OPCs.
Gm56750	unclassified	uncharacterized	Predicted transcript; co-expressed with OPC program.
Olig1	OPC	early OL differentiation	TF driving oligodendrocyte differentiation.
Xylt1	OPC	ECM-modifying OPC	Xylosyltransferase in proteoglycan synthesis during OL development.
Olig2	OPC	canonical OPC	Master TF for OPC specification and OL lineage.
Kazn	OPC	cytoskeletal OPC	Kazrin; expressed in OL lineage cells.
Lims2	OPC	adhesion/cytoskeleton	LIM domain protein enriched in OL lineage.
Mpzl1	OPC	adhesion OPC	Myelin protein zero–like 1; present in early OL lineage.
Marcks	OPC	cytoskeletal signaling	Myristoylated alanine-rich C kinase substrate in OPCs and astrocytes.
Tcf7l2	OPC	differentiating OL	TF driving transition from OPC to myelinating OL.
Thra	OPC	differentiating OL	Thyroid hormone receptor α; promotes OL maturation.
Slc44a1	OPC	choline transporter	Choline transporter-like 1; supports myelin lipid synthesis.
Tmem163	OPC	vesicle transport	Cation transporter expressed in OL lineage cells.
Agap1	OPC	endocytic trafficking	ArfGAP; vesicular transport in OL lineage cells.

This set is almost entirely OPC-focused, with hallmark markers (Pdgfra, Olig1, Olig2) and genes for cytoskeletal remodeling, vesicle/endocytic trafficking, and differentiation signaling (Tcf7l2, Thra, Slc44a1). Occasional neuronal genes (Cacng4, Nxph1) are likely due to minor contamination. Overall, this cluster represents proliferating and early differentiating oligodendrocyte precursor cells.

7.2.2.25 Cluster 26

Gene	Cell	Subtype	Notes
Gria4	neuron	excitatory neuron (granule/IT)	AMPA receptor GluA4; enriched in cerebellar granule and cortical excitatory neurons.
Acsbg1	astrocyte	metabolic astrocyte	Long-chain acyl-CoA synthetase; astrocyte-enriched lipid metabolism.
Stk32a	neuron	excitatory neuron (granule-biased)	Kinase enriched in cerebellar granule and select cortical excitatory neurons.
Timp4	neuron	excitatory neuron	Synaptic/ECM regulator with neuronal enrichment.
Grid2	neuron	Purkinje neuron	Glutamate receptor δ2; Purkinje cell hallmark.
Tril	astrocyte	innate immune/BBB-adjacent astrocyte	TLR4 accessory protein induced in astrocytes.
Rgs7bp	neuron	synaptic signaling neuron	Anchor for RGS7–Gβ5 complexes at neuronal membranes.
Lama2	astrocyte	perivascular/endfoot astrocyte	Laminin α2 secreted by astrocyte endfeet at the BBB.
Pals2	neuron	postsynaptic scaffold	MAGUK family (MPP6) at neuronal junctions.
Cap2	neuron	excitatory neuron	Actin regulator in dendrites/axons; neuronal enriched.
Hdac8	neuron	generic neuron	Histone deacetylase with neuronal expression in CNS.
Ank2	neuron	axonal/somatic neuron	Ankyrin-B; neuronal cytoskeleton and membrane domain organization.
Fam107a	astrocyte	stress-responsive astrocyte	DRR1; glia-enriched, actin/stress program.
Ust	oligodendrocyte	differentiating OL	Chondroitin/dermatan 2-sulfotransferase; OL/ECM remodeling.
Gpm6b	oligodendrocyte	myelinating oligodendrocyte	Myelin-associated membrane glycoprotein (also in neurons).
Paqr6	neuron	excitatory neuron	Progestin/adipoQ receptor; neuron-biased expression.
Sema6d	neuron	excitatory neuron	Axon-guidance semaphorin in developing projection neurons.
Omg	oligodendrocyte	myelin/axon-inhibitory	Oligodendrocyte myelin glycoprotein; myelin-associated inhibitor.
Prkca	neuron	excitatory neuron	PKCα; postsynaptic signaling in pyramidal neurons.
Slc38a3	astrocyte	protoplasmic astrocyte	SNAT3 glutamine transporter; astrocyte-enriched at synapses.

Cluster 26 is neuron-dominant with strong excitatory and Purkinje signatures (Gria4, Grid2, Prkca, Rgs7bp). Astrocyte endfoot and metabolic markers are present (Acsbg1, Lama2, Slc38a3, Tril, Fam107a). Several myelin/OL genes (Omg, Gpm6b, Ust) indicate minor oligodendrocyte admixture. Overall, this cluster reflects excitatory/Purkinje-related neurons at the neurovascular–myelin interface.

7.2.2.26 Cluster 27

Gene	Cell	Subtype	Notes
Cavin1	smooth muscle	vascular SMC/pericyte	Caveolae scaffold (PTRF) abundant in mural cells.
Ltbp1	perivascular fibroblast	vascular fibroblast	TGF-β latent complex binder; ECM-rich fibroblasts.
Tpm1	smooth muscle	vascular SMC	Contractile tropomyosin isoform in SMC.
Mylk	smooth muscle	vascular SMC	Myosin light chain kinase driving contraction.
Crim1	perivascular fibroblast	vascular fibroblast	ECM/adhesion protein in stromal perivascular cells.
Tpm2	smooth muscle	vascular SMC	Contractile tropomyosin in mural cells.
Pde3a	smooth muscle	vascular SMC	cAMP PDE enriched in contractile SMC.
Rasd1	smooth muscle	vascular SMC/pericyte (IEG)	Ras GTPase induced by glucocorticoids/NO in mural cells.
Palld	smooth muscle	vascular SMC/pericyte	Palladin; actin cytoskeleton/contractile apparatus.
Ogn	perivascular fibroblast	vascular fibroblast	Osteoglycin; matrix proteoglycan around vessels.
Rbpms	smooth muscle	vascular SMC/pericyte	RNA-binding protein seen in mural lineages; RGC in retina.
Crip1	perivascular fibroblast	vascular fibroblast	LIM zinc-binding protein enriched in stromal fibroblasts.
Enah	smooth muscle	vascular SMC/pericyte	Actin regulator supporting contractile structures.
Ccn3	perivascular fibroblast	vascular fibroblast	NOV; matricellular regulator in vessel-adjacent stroma.
Rcan2	smooth muscle	vascular SMC/pericyte	Calcineurin modulator in vascular cells.
Slc38a2	pericyte	capillary pericyte	SNAT2 amino-acid transporter expressed in mural cells.
Csrp1	smooth muscle	vascular SMC	LIM protein in contractile SMC cytoskeleton.
Neo1	perivascular fibroblast	vascular fibroblast	Neogenin receptor in perivascular mesenchyme/ECM guidance.
Efemp1	perivascular fibroblast	vascular fibroblast	Fibulin-3; ECM protein in perivascular fibroblasts.
Fxyd5	perivascular fibroblast	vascular fibroblast	Dysadherin; stromal/vascular surface glycoprotein.

The set maps to the neurovascular unit, dominated by mural cells. Strong contractile genes define vascular smooth muscle and pericytes (Tpm1/2, Mylk, Pde3a, Palld, Csrp1, Cavin1, Rasd1, Enah, Rcan2). A parallel ECM/matricellular module marks perivascular fibroblasts (Ltbp1, Ogn, Ccn3, Efemp1, Crip1, Neo1, Fxyd5). Slc38a2 supports a pericyte metabolic role. Overall, this cluster represents contractile mural cells with a prominent perivascular fibroblast component.

7.2.2.27 Cluster 28

Gene	Cell	Subtype	Notes
Birc5	cycling cell	G2/M phase	Survivin; mitotic regulator in proliferating cells.
Cdca8	cycling cell	G2/M phase	Borealin; chromosome passenger complex component in mitosis.
Tpx2	cycling cell	G2/M phase	Spindle assembly factor during mitosis.
Mki67	cycling cell	all cycling phases	Canonical proliferation marker.
Cenpe	cycling cell	G2/M phase	Kinetochore motor protein essential for chromosome alignment.
Cenpf	cycling cell	G2/M phase	Kinetochore protein in late mitosis.
Top2a	cycling cell	G2/M phase	DNA topoisomerase IIα; chromosome segregation.
Cenpa	cycling cell	G2/M phase	Centromeric histone variant in dividing cells.
Ube2c	cycling cell	G2/M phase	Ubiquitin-conjugating enzyme for mitotic progression.
Hmmr	cycling cell	G2/M phase	RHAMM; spindle-associated protein.
Knl1	cycling cell	G2/M phase	Kinetochore scaffold protein.
H3c3	cycling cell	S–G2/M phase	Histone H3 variant expressed in dividing cells.
Pbk	cycling cell	G2/M phase	PDZ-binding kinase; mitotic kinase in progenitors.
Prc1	cycling cell	G2/M phase	Cytokinesis regulator in proliferating cells.
Nusap1	cycling cell	G2/M phase	Microtubule bundling protein during mitosis.
Aspm	cycling cell	G2/M phase	Spindle pole protein in neural progenitors.
Kif23	cycling cell	G2/M phase	Cytokinesis kinesin.
Ifi27l2a	cycling cell	interferon-responsive cycling cell	ISG upregulated in some proliferating immune/glial cells.
Rrm2	cycling cell	S phase	Ribonucleotide reductase subunit in DNA synthesis.
Gm42047	unclassified	uncharacterized	Predicted gene; likely co-expressed with cycling programs.

Cluster 28 is a pure proliferation/cell-cycle signature, dominated by G2/M phase and mitotic spindle/kinetochore genes (Birc5, Mki67, Top2a, Cenp family, Tpx2, Nusap1). The profile fits actively dividing cells from multiple lineages—likely cycling OPCs, microglia, or endothelial cells—rather than a distinct mature cell type. Ifi27l2a suggests some interferon-responsive cycling cells.

7.2.2.28 Cluster 29

Gene	Cell	Subtype	Notes
Otx2os1	neuron	excitatory neuron (midbrain/forebrain)	lncRNA near Otx2; linked to midbrain/forebrain neuronal identity.
Fras1	ependymal	choroid plexus epithelium	ECM protein enriched in ventricular/choroid plexus cells.
Folr1	ependymal	choroid plexus epithelium	Folate receptor α; hallmark of choroid plexus epithelial cells.
Prlr	astrocyte	neuroendocrine-responsive astrocyte	Prolactin receptor expressed in hypothalamic/limbic astrocytes.
Kcne2	ependymal	choroid plexus epithelium	Potassium channel β-subunit enriched in CSF-secreting cells.
Wfdc2	ependymal	choroid plexus epithelium	HE4; secreted protease inhibitor from choroid plexus epithelium.
Vat1l	neuron	excitatory neuron	Synaptic vesicle protein abundant in neurons.
Spint2	ependymal	choroid plexus epithelium	Serine protease inhibitor in epithelial barrier cells.
Nhsl2	neuron	excitatory neuron	Actin cytoskeleton regulator enriched in neurons.
Pip5k1b	neuron	excitatory neuron	Phosphatidylinositol-4-phosphate kinase; neuronal expression.
Htr2c	neuron	excitatory neuron	Serotonin receptor 2C; postsynaptic receptor in neurons.
Tmem72	ependymal	choroid plexus epithelium	Transmembrane protein highly enriched in choroid plexus.
F5	endothelial	vascular endothelium	Coagulation factor V produced by CNS endothelium.
Slc4a10	neuron	excitatory neuron	Sodium-bicarbonate transporter in neurons, especially inhibitory/excitatory interface.
Prdm16	neuron	excitatory neuron	TF in neuronal subtype specification.
Slc4a5	ependymal	choroid plexus epithelium	Sodium-bicarbonate transporter in CSF-secreting epithelial cells.
Atp2b3	neuron	excitatory neuron	PMCA3 Ca²⁺ pump enriched in neurons.
Sh3d19	neuron	excitatory neuron	SH3 domain protein enriched in neuronal tissue.
Lbp	endothelial	vascular endothelium	LPS-binding protein expressed in vascular cells.
Tmem98	ependymal	choroid plexus epithelium	Transmembrane protein with high choroid plexus specificity.

This set shows a dual identity: a strong choroid plexus/ependymal epithelium signature (Folr1, Wfdc2, Kcne2, Spint2, Tmem72, Slc4a5, Fras1, Tmem98) alongside neuronal genes (Otx2os1, Vat1l, Htr2c, Slc4a10, Atp2b3). Endothelial markers (F5, Lbp) suggest vascular contact. Overall, the dominant signal points to choroid plexus epithelial cells, with some neuronal admixture likely from nearby tissue or partial doublets.

7.2.3 Grouping of clusters by major cell class and most likely subtype

Group	Clusters	Main Subtype(s)	Summary Notes
Excitatory neurons	17, 26	Cortical/hippocampal pyramidal, Purkinje, granule neurons	Glutamatergic projection neurons with regional specializations (Grin2a, Grid2, Gria4).
Inhibitory neurons	20	Developing GABAergic interneurons	Dlx1/2, Arx, Sp9 define immature inhibitory lineage despite some excitatory markers.
Astrocytes	10, 11	Protoplasmic, perivascular/ECM astrocytes	GABA handling (Slc6a11, Abat) and ECM/vascular interaction (Sparc, Lama2, Gfap).
Oligodendrocytes (mature)	4, 9	Myelinating OLs	Myelin/lipid programs (Aspa, Abca2, Ermn, Gjb1, Klk6, Trf).
OPCs and newly formed OLs	25	OPC → NFOL	Pdgfra, Olig1/2, Lpar1; early myelin and lipid synthesis genes.
Microglia — homeostatic	5	Homeostatic microglia	P2ry12, Siglech define resident microglia in resting state.
Microglia — activated/DAM	0, 1, 2, 3, 8, 12, 14	DAM, MHC-II+, IFN-responsive microglia	Trem2/Spp1, MHC-II genes (H2, Cd74), ISGs (Mx1/Ifit), lipid and iron metabolism, hypoxia responses (Hif1a, P4ha1).
Perivascular/border-associated macrophages (BAM)	22	Mrc1⁺Cd163⁺ BAM	M2-like scavenging profile (Maf, Tsc22d3, Stab1, Fcgr2b) at vascular interface.
Endothelial cells	6	Capillary/venous endothelium	Tight junction (Ocln), caveolae (Cav2), metabolic transporters (Slc16a4).
Pericytes & vascular smooth muscle cells (SMC)	19	Capillary pericytes, arteriolar SMC	Contractile and ion channel genes (Pdgfrb, Abcc9/Kcnj8, Myh11, Tagln).
Perivascular fibroblasts	27	ECM-rich vascular fibroblasts	Matrix proteins (Dcn, Aspn, Efemp1, Ltbp1, Ogn) around vessels.
Ependymal/choroid plexus	16, 24, 28	Motile ciliated ependyma, choroid plexus epithelium	Foxj1-driven ciliogenesis (Cfap family) and secretory CP markers (Ttr, Folr1, Wfdc2).
T lymphocytes	15	CD8⁺ tissue-resident/effector T cells	TCR complex (Cd3e/g, Trac), cytotoxic markers (Cd8b1, Runx3, Ctsw), Cxcr6 TRM.
Mixed neurovascular interface	13, 23	Neuron–endothelial–microglia/pericyte niche	Combination of neuronal, endothelial, and pericyte/microglia genes indicating vessel-associated mixed cell populations.
Proliferating cells	28	Cycling progenitors (multiple lineages)	Pure cell-cycle module (Mki67, Top2a, Cenp family) without a single mature identity.